Earlier this month, President Obama issued an executive order establishing a process for reviewing whether prisoners held at Guantanamo Bay continue to pose a threat. Under this order, those who have not been charged with a crime may continue to be detained indefinitely, and may come before a review board every three years, which will evaluate whether continued incarceration is necessary for public safety.

The order is a striking development because, not only has President Obama effectively adopted yet another cornerstone of President Bushs terrorism policy, but he did so unilaterally by executive order, providing detainees solely an executive branch review. But Guantanamo inmates still have a constitutional right to ask federal judges to evaluate the legality of their imprisonment and for two years, the president and Congress have been ignoring their inter-branch responsibility to structure those detention hearings. Now, will they finally act?

In 2008, the Supreme Court ruled in Boumediene v. Bush that detainees held at Guantanamo could file habeas petitions in U.S. courts to contest their detention. But the court left many fundamental questions unanswered. Must a detainee pose a threat in order to be held? Can someone be detained who provided substantial support to a terrorist network even if it was not shown that he was a member? What evidence should be allowed? What should be the burden of proof? May a judge release a detainee into the United States if he clears him for discharge? At the heart of each of these questions lies a fundamental inquiry about how to balance liberty and national security in counterterrorism policies.

National security experts, scholars, judges and politicians urged Congress to enact rules to govern these court proceedings. But for two years, the Democratic Congress did nothing. The response of the chairman of the Senate Judiciary Committee, Democratic Sen. Patrick Leahy of Vermont, was to throw up his hands: “I dont know how wed ever get anything this complex and get the kind of consensus needed to get something passed.”

As a result, judges were left to tackle the crucial and unprecedented task of creating a new set of rules to review military capture and detention decisions in wartime. But courts are ill-suited for this undertaking. First, this is a task best approached comprehensively. So each policy choice may have a countervailing affect on another (e.g. opting for a high burden of proof might be balanced by permitting lenient evidence rules). But judges cannot set up comprehensive policy. They may only decide the particular issue in the case before them and are restricted to viewing only the facts presented.

Second, common law develops at a glacial pace. A literal system of trial and error, it may take several years for a case to make its way up through the appeals process. When it does, the higher court may rule on only one discrete issue and remand the case for further fact-finding. All the while, our national security apparatus is paralyzed by legal uncertainty. Finally, each of these decisions is, at bottom, a balance of liberty and security - a paradigmatic policy choice that should be made by democratically elected officials rather than unelected judges.

Indeed, the judicial branch itself has been pleading for guidance from the political branches. Judge Raymond Randolph of the U.S. Court of Appeals for the District of Columbia Circuit recently called the post-Boumediene jurisprudence the “Guantanamo Mess.” And Judge Janice Rogers Brown, who sits on the same court, explicitly asked Congress to step in: “The circumstances that frustrate the judicial process are the same ones that make this situation particularly ripe for Congress to intervene pursuant to its policy expertise, democratic legitimacy and oath to uphold and defend the Constitution. These cases present hard questions and hard choices, ones best faced directly. Judicial review, however, is just that: re-view, an indirect and necessarily backward looking process.” This unprecedented task, she said, “demands new rules be written.”

But with no guidance from Congress or the president, it is no surprise that two-and-a-half years after Boumediene, the new doctrine is unsettled and uncertain. Just recently, the first petitions made their way up the appeals chain to the Supreme Court, which is being asked to decide a wide range of issues, from specific procedural inquiries to broad substantive matters. For example, in Al Odah v. United States, the issue is whether establishing guilt by a preponderance of the evidence suffices and whether secondhand statements should be admissible. Kiyemba v. Obama presents the crucial separation-of-powers question of whether a judge can order the release of a detainee into the United States over the objection of the president. And in Al Bahani v. Obama, there is the fundamental question of whether the president has statutory power to hold indefinitely a prisoner captured on the battlefield in Afghanistan, now that the Taliban government is not in power.

The courts will be asked to grapple with such issues for years if not decades, if they are not given guidance by the political branches. And in the meantime, the uncertainty and unpredictability harms all concerned. Soldiers on the battlefield do not know what evidence and circumstances legally justify capture and detention. And detainees who have been cleared for discharge may be left in limbo for years as the courts work out a process for their release.

Now that Mr. Obama may have abandoned his Panglossian fantasy of closing Guantanamo Bay, he must work with Congress to enact substantive and procedural rules for prisoners challenging their confinement. And with new leadership in the House, there is hope that the difficult work of legislating a sensible detention policy may finally begin.